Predicting the critical nucleus size and the nucleation barrier is of central importance in controlling the dynamics of nucleation. However, as the nucleation of a crystal involves intermediate states, the prediction becomes inaccessible with currently available models. Here, we show that based on single-particle level observations, the properties of crystal nuclei in a microscopic stepwise nucleation (MSN) can be well-quantified by incorporating the size and structure order parameter into the formula of free energy without prior knowledge of interfacial tension. The quantified free energy reveals that the intermediate structures arise from thermodynamics rather than kinetics. Precritical and postcritical nuclei are distinct not only in structure but also in the mechanism of crystalline ordering. The relative stability of intermediate structures and the pathway of nucleation can be well-controlled by supercooling. Our studies offer a successful approach to quantify MSN and shed new light on resolving the long-standing discrepancies between simulations and experiments.